class Bio::Fasta::Report::Hit

Attributes

definition[R]

query[R]

score[R]

target[R]

Public Class Methods

new(data) click to toggle source

    # File lib/bio/appl/fasta/format10.rb
202 def initialize(data)
203   score, query, target = data.split(/\n>/)
204 
205   @definition, *score = score.split(/\n/)
206   @score = {}
207 
208   pat = /;\s+([^:]+):\s+(.*)/
209 
210   score.each do |x|
211     if pat.match(x)
212       @score[$1] = $2
213     end
214   end
215 
216   @query = Query.new(query)
217   @target = Target.new(target)
218 end

Public Instance Methods

bit_score() click to toggle source

Bit score

    # File lib/bio/appl/fasta/format10.rb
235 def bit_score
236   if @score['fa_bits']
237     @score['fa_bits'].to_f
238   elsif @score['sw_bits']
239     @score['sw_bits'].to_f
240   elsif @score['fx_bits']
241     @score['fx_bits'].to_f
242   elsif @score['tx_bits']
243     @score['tx_bits'].to_f
244   end
245 end

direction() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
247 def direction
248   @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame']
249 end

evalue() click to toggle source

E-value score

    # File lib/bio/appl/fasta/format10.rb
222 def evalue
223   if @score['fa_expect']
224     @score['fa_expect'].to_f
225   elsif @score['sw_expect']
226     @score['sw_expect'].to_f
227   elsif @score['fx_expect']
228     @score['fx_expect'].to_f
229   elsif @score['tx_expect']
230     @score['tx_expect'].to_f
231   end
232 end

identity() click to toggle source

percent identity

    # File lib/bio/appl/fasta/format10.rb
257 def identity
258   @score['sw_ident'].to_f
259 end

lap_at() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
328 def lap_at
329   [ query_start, query_end, target_start, target_end ]
330 end

overlap() click to toggle source

overlap length

    # File lib/bio/appl/fasta/format10.rb
262 def overlap
263   @score['sw_overlap'].to_i
264 end

query_def() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
276 def query_def
277   @query.definition
278 end

query_end() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
316 def query_end
317   @query.stop
318 end

query_id() click to toggle source

Shortcuts for the methods of Bio::Fasta::Report::Hit::Query

    # File lib/bio/appl/fasta/format10.rb
268 def query_id
269   @query.entry_id
270 end

query_len() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
284 def query_len
285   @query.length
286 end

query_seq() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
294 def query_seq
295   @query.sequence
296 end

query_start() click to toggle source

Information on matching region

    # File lib/bio/appl/fasta/format10.rb
312 def query_start
313   @query.start
314 end

query_type() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
302 def query_type
303   @query.moltype
304 end

sw() click to toggle source

Smith-Waterman score

    # File lib/bio/appl/fasta/format10.rb
252 def sw
253   @score['sw_score'].to_i
254 end

target_def() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
280 def target_def
281   @target.definition
282 end

target_end() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
324 def target_end
325   @target.stop
326 end

target_id() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
272 def target_id
273   @target.entry_id
274 end

target_len() click to toggle source

Shortcuts for the methods of Bio::Fasta::Report::Hit::Target

    # File lib/bio/appl/fasta/format10.rb
290 def target_len
291   @target.length
292 end

target_seq() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
298 def target_seq
299   @target.sequence
300 end

target_start() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
320 def target_start
321   @target.start
322 end

target_type() click to toggle source

    # File lib/bio/appl/fasta/format10.rb
306 def target_type
307   @target.moltype
308 end